Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012085.1 Corchorus olitorius cultivar O-4 contig12118, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13812
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:480 original size:54 final size:54
Alignment explanation
Indices: 421--524 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
411 TGGATGACCG
421 GTAATTGGCTTAAAACTTGACGGGTTGTGCCGCACAGGGGAGAGATGAGGGCCA
1 GTAATTGGCTTAAAACTTGACGGGTTGTGCCGCACAGGGGAGAGATGAGGGCCA
*
475 GTAATTGGCTTAAAACTTGACGGGTTGTGCCGCACGGGGGAGAGATGAGG
1 GTAATTGGCTTAAAACTTGACGGGTTGTGCCGCACAGGGGAGAGATGAGG
525 ACTCACAAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.21
Consensus pattern (54 bp):
GTAATTGGCTTAAAACTTGACGGGTTGTGCCGCACAGGGGAGAGATGAGGGCCA
Found at i:1795 original size:2 final size:2
Alignment explanation
Indices: 1790--1822 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1780 AATTTTTTAG
1790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1823 CATTCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2049 original size:27 final size:27
Alignment explanation
Indices: 1969--2061 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
1959 AAACCAAGGG
* * *
1969 GGTTATGGAGGTTATGGTGGACGTGGA
1 GGTTATGGAGGGTACGGTGGACGTGGC
*
1996 GGTAATGGAGGGTACGGTGGACGTGGC
1 GGTTATGGAGGGTACGGTGGACGTGGC
*
2023 GGTTATGGAGGGTACGGTGGCCGTGGC
1 GGTTATGGAGGGTACGGTGGACGTGGC
* *
2050 GGCTACGGAGGG
1 GGTTATGGAGGG
2062 CGCGGTGGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.16, C:0.11, G:0.52, T:0.22
Consensus pattern (27 bp):
GGTTATGGAGGGTACGGTGGACGTGGC
Found at i:2089 original size:18 final size:18
Alignment explanation
Indices: 2028--2097 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 18
2018 GTGGCGGTTA
*
2028 TGGAGGGTACGGTGGCCG
1 TGGAGGGTACGGTGGACG
* * * *
2046 TGGCGGCTACGGAGGGCG
1 TGGAGGGTACGGTGGACG
* *
2064 CGGTGGGTACGGTGGACG
1 TGGAGGGTACGGTGGACG
*
2082 TGGAGGGTATGGTGGA
1 TGGAGGGTACGGTGGA
2098 GGCTGCGCCT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.13, C:0.14, G:0.56, T:0.17
Consensus pattern (18 bp):
TGGAGGGTACGGTGGACG
Found at i:3252 original size:7 final size:7
Alignment explanation
Indices: 3240--3285 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
3230 AAACTCATTA
3240 TATATAC
1 TATATAC
3247 TATATAC
1 TATATAC
3254 TATATAC
1 TATATAC
3261 TATATAC
1 TATATAC
3268 TATATAC
1 TATATAC
3275 TATATAC
1 TATATAC
3282 TATA
1 TATA
3286 CTATACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (7 bp):
TATATAC
Found at i:3557 original size:56 final size:57
Alignment explanation
Indices: 3474--3587 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 57
3464 ATCCGTTTCT
* * *
3474 TTTCACACAATAAATATTATAATAAATCGTAT-CCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATATCATAATAAATCCTATCCCCCCTATCTATACTTAATTATTC
3530 TTTCACACAATAAATATCATAATAAATCCTATCCCCCCTATCTATACTTAATTATTC
1 TTTCACACAATAAATATCATAATAAATCCTATCCCCCCTATCTATACTTAATTATTC
3587 T
1 T
3588 ATAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 30 0.56
57 24 0.44
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.39
Consensus pattern (57 bp):
TTTCACACAATAAATATCATAATAAATCCTATCCCCCCTATCTATACTTAATTATTC
Found at i:3603 original size:57 final size:56
Alignment explanation
Indices: 3482--3600 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 56
3472 CTTTTCACAC
* * * * * * *
3482 AATAAATATTATAATAAATCGTATCCCCCTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATATCATAATAAATCCTATCCCCCTATCTATACTTAATTATTCTATAAAAA
3538 AATAAATATCATAATAAATCCTATCCCCCCTATCTATACTTAATTATTCTATAAAATA
1 AATAAATATCATAATAAATCCTAT-CCCCCTATCTATACTTAATTATTCTATAAAA-A
3596 AATAA
1 AATAA
3601 TATTTTCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
56 22 0.41
57 27 0.50
58 5 0.09
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (56 bp):
AATAAATATCATAATAAATCCTATCCCCCTATCTATACTTAATTATTCTATAAAAA
Found at i:3712 original size:42 final size:42
Alignment explanation
Indices: 3653--3732 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
3643 TAAGGATCAG
3653 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
3695 GATTTTAGTTGAGTATTTCTTAATTTACAGAGAATTTT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTT
3733 TAAGAGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:5151 original size:17 final size:17
Alignment explanation
Indices: 5104--5154 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
5094 TGCCACATGC
*
5104 ATGACTGATAATGTTTT
1 ATGACTAATAATGTTTT
* * * *
5121 ATTACCATTCATGTTTT
1 ATGACTAATAATGTTTT
5138 ATGACTAATAATGTTTT
1 ATGACTAATAATGTTTT
5155 CCTCTTCAAA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (17 bp):
ATGACTAATAATGTTTT
Found at i:5723 original size:21 final size:24
Alignment explanation
Indices: 5664--5744 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 24
5654 TTTAGTAATT
* *
5664 AAATATGTATTATTTATTTATTTTG
1 AAATATATATTA-TTATTTATTTAG
*
5689 AACTCAT-TA-T-TTA-TTATTTA-
1 AAAT-ATATATTATTATTTATTTAG
5709 AAATATAT-TTATTATTTATTTAG
1 AAATATATATTATTATTTATTTAG
*
5732 TAATATATATTAT
1 AAATATATATTAT
5745 ATCTAATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 9 0.20
22 10 0.22
23 7 0.16
24 5 0.11
25 5 0.11
26 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
AAATATATATTATTATTTATTTAG
Found at i:5739 original size:25 final size:25
Alignment explanation
Indices: 5694--5742 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5684 TTTTGAACTC
*
5694 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATGTAAAATATATTT
*
5719 ATTATTTATT-TAGTAATATATATT
1 ATTATTTATTAT-GTAAAATATATT
5743 ATATCTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATGTAAAATATATTT
Found at i:6190 original size:13 final size:13
Alignment explanation
Indices: 6172--6197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6162 CTATATCTAA
6172 GTATCAGAAAGGT
1 GTATCAGAAAGGT
6185 GTATCAGAAAGGT
1 GTATCAGAAAGGT
6198 CCCTTCTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
GTATCAGAAAGGT
Found at i:6724 original size:217 final size:216
Alignment explanation
Indices: 6342--6759 Score: 746
Period size: 217 Copynumber: 1.9 Consensus size: 216
6332 TTGTAATTAG
* **
6342 GTGAAATTACTAAATGCTCCTTCTAACTTTTAATTTGGGATGACCTTATCGCCCTGTTTTAGTCA
1 GTGAAAGTACTAAATGCTCCTTCTAACTTTTAACATGGGATGACCTTATCGCCCTGTTTTAGTCA
* *
6407 TTTCTCACATGCGGTTACATTGAACCGATTCGTATTCCATCACTCTATAACCTCATAAATCATAT
66 TTTCTCACATGCGATTACACTGAACCGATTCGTATTCCATCACTCTATAACCTCATAAATCATAT
*
6472 TTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACCGAGCAAAAAAAACAATCTATAAAA
131 TTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGC-AAAAAAACAATCTATAAAA
6537 ATTGACTCTACATATTAGTTTA
195 ATTGACTCTACATATTAGTTTA
*
6559 GTGAAAGTACTAAATGCTCCTTCTAACTTTTAACATGGGGTGACCTTATCGCCCTGTTTTAGTCA
1 GTGAAAGTACTAAATGCTCCTTCTAACTTTTAACATGGGATGACCTTATCGCCCTGTTTTAGTCA
*
6624 TTTCTCACATGCGATTACACTGAATCGATTCGTATTCCATCACTCTATAACCTCATAAATCATAT
66 TTTCTCACATGCGATTACACTGAACCGATTCGTATTCCATCACTCTATAACCTCATAAATCATAT
*
6689 TTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGCAAAAAAATAATCTATAAAAA
131 TTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGCAAAAAAACAATCTATAAAAA
6754 TTGACT
196 TTGACT
6760 TATATGATAA
Statistics
Matches: 192, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
216 25 0.13
217 167 0.87
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (216 bp):
GTGAAAGTACTAAATGCTCCTTCTAACTTTTAACATGGGATGACCTTATCGCCCTGTTTTAGTCA
TTTCTCACATGCGATTACACTGAACCGATTCGTATTCCATCACTCTATAACCTCATAAATCATAT
TTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGCAAAAAAACAATCTATAAAAA
TTGACTCTACATATTAGTTTA
Found at i:7463 original size:15 final size:15
Alignment explanation
Indices: 7443--7474 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7433 GAATATATTT
*
7443 TTTTTAAATGATCTA
1 TTTTTAAATGATATA
7458 TTTTTAAATGATATA
1 TTTTTAAATGATATA
7473 TT
1 TT
7475 ATGATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTTTAAATGATATA
Found at i:9373 original size:118 final size:118
Alignment explanation
Indices: 9165--9395 Score: 417
Period size: 118 Copynumber: 2.0 Consensus size: 118
9155 GAAGAACATT
* * * *
9165 CACCACAATCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACTAACT
1 CACCACAACCATGAATATTGTTCTGAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAACT
9230 CTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTC
66 CTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTC
*
9283 CACCACAACCATGAATATTGTTCTGAAGAATTTCAAGTCCTTGAATTTTCCACTTCAAACCAACT
1 CACCACAACCATGAATATTGTTCTGAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAACT
9348 CTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
66 CTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
9396 CGCGTTAACA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 108 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (118 bp):
CACCACAACCATGAATATTGTTCTGAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAACT
CTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTC
Found at i:10324 original size:28 final size:28
Alignment explanation
Indices: 10284--10339 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
10274 CTTAAGGTTC
10284 ACATGGTATATATGTGTGTGTGTGTGTG
1 ACATGGTATATATGTGTGTGTGTGTGTG
10312 ACATGGTATATATGTGTGTGTGTGTGTG
1 ACATGGTATATATGTGTGTGTGTGTGTG
10340 TGTATAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.43
Consensus pattern (28 bp):
ACATGGTATATATGTGTGTGTGTGTGTG
Found at i:12667 original size:25 final size:26
Alignment explanation
Indices: 12621--12669 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
12611 GGCCAGCAAG
12621 GCGCGGCCCAAGCACTTGGCCCAGGC
1 GCGCGGCCCAAGCACTTGGCCCAGGC
* *
12647 GCGCGGGCC-AGCGCTTGGCCCAG
1 GCGCGGCCCAAGCACTTGGCCCAG
12670 CGCCTAGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.12, C:0.41, G:0.39, T:0.08
Consensus pattern (26 bp):
GCGCGGCCCAAGCACTTGGCCCAGGC
Found at i:12679 original size:24 final size:24
Alignment explanation
Indices: 12635--12687 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
12625 GGCCCAAGCA
*
12635 CTTGGCCCAGGCGCGCGGGCCAGCG
1 CTTGGCCCAGGCGCGCAGGCCAG-G
12660 CTTGGCCCA-GCGC-CTAGGCCAGG
1 CTTGGCCCAGGCGCGC-AGGCCAGG
12683 CTTGG
1 CTTGG
12688 GCCCCAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 10 0.38
25 9 0.35
ACGTcount: A:0.09, C:0.38, G:0.40, T:0.13
Consensus pattern (24 bp):
CTTGGCCCAGGCGCGCAGGCCAGG
Found at i:13644 original size:28 final size:28
Alignment explanation
Indices: 13613--13687 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
13603 TTAAGATATC
* *
13613 AAAATTACTGTTTTGCCCTTGGTCAGCT
1 AAAATTACAGTTTTGCCCTTGGTCAACT
* * *
13641 AAAATTACCA-TTTTACCCCTGGTTAACT
1 AAAATTA-CAGTTTTGCCCTTGGTCAACT
13669 -AAATTACAGTTTTGCCCTT
1 AAAATTACAGTTTTGCCCTT
13688 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
28 21 0.55
29 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTGCCCTTGGTCAACT
Done.